Zeyneb Kurt
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Mergeomics |
| git_branch: devel |
| git_last_commit: df484e2 |
| git_last_commit_date: 2024-04-30 10:48:10 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1167/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Mergeomics 1.33.0 (landing page) Zeyneb Kurt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the Mergeomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mergeomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Mergeomics |
| Version: 1.33.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.33.0.tar.gz |
| StartedAt: 2024-06-10 05:55:03 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 06:14:56 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 1192.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Mergeomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Mergeomics.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.33.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Mergeomics’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.3Mb
sub-directories of 1Mb or more:
extdata 7.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kda.analyze: no visible global function definition for ‘p.adjust’
kda.analyze.exec: no visible global function definition for ‘pnorm’
kda.analyze.simulate: no visible global function definition for ‘rnorm’
kda.prepare: no visible global function definition for ‘quantile’
kda.prepare: no visible global function definition for ‘object.size’
kda.prepare.screen: no visible global function definition for
‘quantile’
kda.prepare.screen: no visible global function definition for ‘median’
kda.start: no visible global function definition for ‘object.size’
kda2cytoscape: no visible global function definition for ‘write.table’
kda2cytoscape.colormap: no visible global function definition for
‘rainbow’
kda2cytoscape.colormap: no visible global function definition for
‘col2rgb’
kda2himmeli: no visible global function definition for ‘quantile’
kda2himmeli: no visible global function definition for ‘write.table’
kda2himmeli.colormap: no visible global function definition for
‘rainbow’
kda2himmeli.colormap: no visible global function definition for
‘col2rgb’
ssea.analyze: no visible global function definition for ‘qnorm’
ssea.analyze: no visible global function definition for ‘approx’
ssea.analyze: no visible global function definition for ‘pnorm’
ssea.analyze.simulate: no visible global function definition for
‘quantile’
ssea.control: no visible global function definition for ‘median’
ssea.control: no visible global function definition for ‘object.size’
ssea.meta: no visible global function definition for ‘qnorm’
ssea.meta: no visible global function definition for ‘quantile’
ssea.meta: no visible global function definition for ‘pnorm’
ssea.meta: no visible global function definition for ‘median’
ssea.meta: no visible global function definition for ‘na.omit’
ssea.prepare: no visible global function definition for ‘median’
ssea.prepare: no visible global function definition for ‘object.size’
ssea.start: no visible global function definition for ‘na.omit’
ssea.start: no visible global function definition for ‘object.size’
ssea.start.configure: no visible global function definition for
‘write.table’
ssea2kda: no visible global function definition for ‘na.omit’
ssea2kda.import: no visible global function definition for ‘na.omit’
tool.aggregate: no visible global function definition for ‘na.omit’
tool.cluster: no visible global function definition for ‘as.dist’
tool.cluster: no visible global function definition for ‘hclust’
tool.fdr.bh: no visible global function definition for ‘qnorm’
tool.fdr.bh: no visible global function definition for ‘p.adjust’
tool.fdr.bh: no visible global function definition for ‘approx’
tool.fdr.empirical: no visible global function definition for ‘qnorm’
tool.fdr.empirical: no visible global function definition for ‘approx’
tool.metap: no visible global function definition for ‘qnorm’
tool.metap: no visible global function definition for ‘pnorm’
tool.normalize: no visible global function definition for ‘sd’
tool.normalize: no visible global function definition for ‘median’
tool.normalize: no visible global function definition for ‘optim’
tool.normalize: no visible global function definition for ‘ks.test’
tool.normalize.quality: no visible global function definition for ‘sd’
tool.normalize.quality: no visible global function definition for
‘ks.test’
tool.overlap: no visible global function definition for ‘phyper’
tool.read: no visible global function definition for ‘read.delim’
tool.read: no visible global function definition for ‘na.omit’
tool.save: no visible global function definition for ‘write.table’
tool.unify: no visible global function definition for ‘sd’
tool.unify: no visible global function definition for ‘quantile’
tool.unify: no visible global function definition for ‘approx’
Undefined global functions or variables:
approx as.dist col2rgb hclust ks.test median na.omit object.size
optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm
sd write.table
Consider adding
importFrom("grDevices", "col2rgb", "rainbow")
importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median",
"na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm",
"quantile", "rnorm", "sd")
importFrom("utils", "object.size", "read.delim", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kda.analyze.exec 18.787 0.359 21.271
kda.analyze.test 18.769 0.254 20.975
kda.analyze.simulate 18.597 0.240 20.466
kda.prepare 18.562 0.228 20.891
ssea2kda 12.432 0.274 14.460
ssea2kda.analyze 12.148 0.258 14.213
ssea.meta 10.261 0.179 11.395
ssea2kda.import 10.063 0.204 11.559
ssea.finish.details 9.972 0.164 10.987
ssea.analyze 9.863 0.243 11.189
ssea.finish 9.704 0.167 10.866
ssea.finish.fdr 9.702 0.161 10.972
ssea.finish.genes 9.665 0.168 10.901
ssea.analyze.simulate 9.138 0.166 10.338
ssea.prepare 7.630 0.076 8.815
ssea.analyze.observe 7.467 0.074 8.328
ssea.analyze.randloci 7.462 0.071 8.231
ssea.analyze.randgenes 7.453 0.078 8.272
ssea.control 7.323 0.071 8.119
ssea.prepare.counts 7.296 0.073 8.492
ssea.prepare.structure 7.219 0.078 8.267
ssea.start 7.117 0.071 7.861
ssea.start.relabel 7.054 0.080 7.783
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.
Mergeomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Mergeomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Mergeomics’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Mergeomics)
Mergeomics.Rcheck/tests/runTests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("Mergeomics")
KDA Version:12.7.2015
Parameters:
Search depth: 1
Search direction: 1
Maximum overlap: 0.33
Minimum module size: 20
Minimum degree: automatic
Maximum degree: automatic
Edge factor: 0
Random seed: 1
Importing edges...
TAIL HEAD WEIGHT
Length:140663 Length:140663 Min. :1
Class :character Class :character 1st Qu.:1
Mode :character Mode :character Median :1
Mean :1
3rd Qu.:1
Max. :1
Importing modules...
MODULE NODE
Length:1643 Length:1643
Class :character Class :character
Mode :character Mode :character
Graph: 7.694687 Mb
Minimum degree set to 20
Maximum degree set to 278
Collecting hubs...
4002 hubs (15904 nodes)
4876 hubs (25.21%)
Graph: 13.28768 Mb
Analyzing network...
6675: Dhcr7, n=114, p=2.24e-17
6648: Cit, n=20, p=7.89e-01
6643: Pbx4, n=23, p=2.32e-05
5582: Sypl, n=319, p=2.02e-02
4746: Tcf7l2, n=73, p=2.63e-02
4708: Tpte, n=86, p=5.05e-02
4511: Pzp, n=160, p=8.85e-03
4464: Tsc22d3, n=487, p=4.28e-13
4407: Dntt, n=93, p=2.40e-20
4360: Amica1, n=132, p=1.06e-06
4588,..: Lrg1, n=86, p=5.76e-12
MSEA Version:01.04.2016
Parameters:
Permutation type: gene
Permutations: 100
Random seed: 1
Minimum gene count: 10
Maximum gene count: 500
Maximum overlap between genes: 0.33
Importing modules...
MODULE DESCR
Length:20 Length:20
Class :character Class :character
Mode :character Mode :character
MODULE GENE
Length:2906 Length:2906
Class :character Class :character
Mode :character Mode :character
Importing marker values...
MARKER VALUE
Length:76866 Min. : 0.8094
Class :character 1st Qu.: 0.9450
Mode :character Median : 1.1374
Mean : 1.3944
3rd Qu.: 1.4688
Max. :323.0100
Importing mapping data...
GENE MARKER
Length:132705 Length:132705
Class :character Class :character
Mode :character Mode :character
Merging genes containing shared markers...
WARNING! Limited overlap analysis due to large number of groups.
53743/1673535
109560/1673535
165368/1673535
221309/1673535
277343/1673535
332309/1673535
388491/1673535
445163/1673535
500480/1673535
556686/1673535
612295/1673535
668281/1673535
723744/1673535
778190/1673535
832455/1673535
887476/1673535
942232/1673535
997483/1673535
1054428/1673535
1110242/1673535
1165975/1673535
1221882/1673535
1276851/1673535
1332762/1673535
1388222/1673535
1443483/1673535
1499556/1673535
1554187/1673535
1609674/1673535
1665368/1673535
1673535 comparisons
21115 comparisons
13861 comparisons
12880 comparisons
Job: 11.66892 Mb
Preparing data structures...
Job: 17.11777 Mb
Adding positive controls...
Job: 17.42039 Mb
Estimating enrichment...
100/100 cycles
Normalizing scores...
RUNIT TEST PROTOCOL -- Mon Jun 10 06:14:30 2024
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
718.513 15.157 819.471
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.005 | 0.004 | 0.009 | |
| job.kda | 0.029 | 0.007 | 0.040 | |
| kda.analyze | 0.019 | 0.006 | 0.031 | |
| kda.analyze.exec | 18.787 | 0.359 | 21.271 | |
| kda.analyze.simulate | 18.597 | 0.240 | 20.466 | |
| kda.analyze.test | 18.769 | 0.254 | 20.975 | |
| kda.configure | 0.001 | 0.001 | 0.002 | |
| kda.finish | 0.235 | 0.017 | 0.281 | |
| kda.finish.estimate | 0.134 | 0.004 | 0.144 | |
| kda.finish.save | 0.136 | 0.004 | 0.147 | |
| kda.finish.summarize | 0.139 | 0.004 | 0.153 | |
| kda.finish.trim | 0.137 | 0.004 | 0.153 | |
| kda.prepare | 18.562 | 0.228 | 20.891 | |
| kda.prepare.overlap | 0.001 | 0.002 | 0.004 | |
| kda.prepare.screen | 0.000 | 0.002 | 0.002 | |
| kda.start | 2.661 | 0.069 | 3.026 | |
| kda.start.edges | 0.004 | 0.003 | 0.008 | |
| kda.start.identify | 0.009 | 0.002 | 0.013 | |
| kda.start.modules | 0.004 | 0.003 | 0.007 | |
| kda2cytoscape | 0.704 | 0.020 | 0.774 | |
| kda2cytoscape.colorize | 0.000 | 0.000 | 0.001 | |
| kda2cytoscape.colormap | 0.001 | 0.000 | 0.001 | |
| kda2cytoscape.drivers | 0.295 | 0.013 | 0.333 | |
| kda2cytoscape.edges | 0.226 | 0.013 | 0.271 | |
| kda2cytoscape.exec | 0.278 | 0.017 | 0.352 | |
| kda2cytoscape.identify | 0.008 | 0.002 | 0.011 | |
| kda2himmeli | 0.722 | 0.026 | 0.859 | |
| kda2himmeli.colorize | 0.000 | 0.000 | 0.001 | |
| kda2himmeli.colormap | 0.001 | 0.000 | 0.001 | |
| kda2himmeli.drivers | 0.227 | 0.012 | 0.294 | |
| kda2himmeli.edges | 0.234 | 0.013 | 0.276 | |
| kda2himmeli.exec | 0.366 | 0.015 | 0.404 | |
| kda2himmeli.identify | 0.007 | 0.001 | 0.008 | |
| ssea.analyze | 9.863 | 0.243 | 11.189 | |
| ssea.analyze.observe | 7.467 | 0.074 | 8.328 | |
| ssea.analyze.randgenes | 7.453 | 0.078 | 8.272 | |
| ssea.analyze.randloci | 7.462 | 0.071 | 8.231 | |
| ssea.analyze.simulate | 9.138 | 0.166 | 10.338 | |
| ssea.analyze.statistic | 0.001 | 0.001 | 0.001 | |
| ssea.control | 7.323 | 0.071 | 8.119 | |
| ssea.finish | 9.704 | 0.167 | 10.866 | |
| ssea.finish.details | 9.972 | 0.164 | 10.987 | |
| ssea.finish.fdr | 9.702 | 0.161 | 10.972 | |
| ssea.finish.genes | 9.665 | 0.168 | 10.901 | |
| ssea.meta | 10.261 | 0.179 | 11.395 | |
| ssea.prepare | 7.630 | 0.076 | 8.815 | |
| ssea.prepare.counts | 7.296 | 0.073 | 8.492 | |
| ssea.prepare.structure | 7.219 | 0.078 | 8.267 | |
| ssea.start | 7.117 | 0.071 | 7.861 | |
| ssea.start.configure | 0.608 | 0.027 | 0.693 | |
| ssea.start.identify | 0.007 | 0.002 | 0.010 | |
| ssea.start.relabel | 7.054 | 0.080 | 7.783 | |
| ssea2kda | 12.432 | 0.274 | 14.460 | |
| ssea2kda.analyze | 12.148 | 0.258 | 14.213 | |
| ssea2kda.import | 10.063 | 0.204 | 11.559 | |
| tool.aggregate | 0.002 | 0.003 | 0.006 | |
| tool.cluster | 0.033 | 0.002 | 0.039 | |
| tool.cluster.static | 0.001 | 0.001 | 0.002 | |
| tool.coalesce | 0.086 | 0.002 | 0.095 | |
| tool.coalesce.exec | 0.260 | 0.003 | 0.281 | |
| tool.coalesce.find | 0.268 | 0.003 | 0.300 | |
| tool.coalesce.merge | 0.256 | 0.004 | 0.292 | |
| tool.fdr | 0.001 | 0.000 | 0.002 | |
| tool.fdr.bh | 0.001 | 0.001 | 0.002 | |
| tool.fdr.empirical | 0.001 | 0.000 | 0.002 | |
| tool.graph | 2.369 | 0.061 | 2.721 | |
| tool.graph.degree | 2.497 | 0.073 | 2.891 | |
| tool.graph.list | 2.352 | 0.067 | 2.732 | |
| tool.metap | 0.007 | 0.002 | 0.009 | |
| tool.normalize | 0.028 | 0.001 | 0.032 | |
| tool.normalize.quality | 0.022 | 0.001 | 0.026 | |
| tool.overlap | 0.013 | 0.002 | 0.017 | |
| tool.read | 0.394 | 0.013 | 0.455 | |
| tool.save | 0.002 | 0.001 | 0.005 | |
| tool.subgraph | 0.137 | 0.005 | 0.170 | |
| tool.subgraph.find | 0.134 | 0.005 | 0.155 | |
| tool.subgraph.search | 0.135 | 0.004 | 0.146 | |
| tool.subgraph.stats | 0.170 | 0.006 | 0.193 | |
| tool.translate | 0.059 | 0.004 | 0.078 | |
| tool.unify | 0.002 | 0.001 | 0.003 | |